To get the FME running:

On XIPHOID:

MySQL

• create the fms user and password
• grant access to the FME database for fms
• import the FMA into the FME database

  up2date mysql-server
  chkconfig mysql-server on
  # set up root pass and .my.cnf
  mysql -u root mysql -e 'CREATE DATABASE FME;'
  mysql -u root mysql -e "GRANT ALL PRIVILEGES ON FME.* TO fms@localhost;"
  mysql -u root mysql -e "GRANT ALL PRIVILEGES ON FME.* TO fms@'%';"
  mysql -u root mysql -e "UPDATE user SET Password = '4968f18e66de36db' WHERE User = 'fms';"
  mysql FME -u root < /usr/local/data/data13/Protege-backups/fma_p2.dump
  # also install java, etc.
  

Tomcat

The FME requires a specific configuration of Tomcat4 with a custom catalina.policy and server.xml. The easiest way to achieve this is with a catalina_base directory, which is in SubVersion source:fme/trunk

adduser fmeuser
su - fmeuser
svn co svn+ssh://joshuadf@lamina.biostr.washington.edu/src/fme
mv fme fmesrc
cd fmesrc
cp -r catalina_base /home/fmeuser/
cp rebuild-fme.sh /home/fmeuser/
cp tomcat4.conf /home/fmeuser/
ant war
cp FME.war /home/fmeuser/catalina_base/webapps

# install tomcat4, check http://tomcat.apache.org/download-41.cgi for latest
cd /home/fmeuser/
wget http://apache.mirrors.pair.com/tomcat/tomcat-4/v4.1.31/bin/jakarta-tomcat-4.1.31.tar.gz
tar zxvf jakarta-tomcat-4.1.31.tar.gz
rm -f jakarta-tomcat-4.1.31.tar.gz
ln -s jakarta-tomcat-4.1.31 tomcat4
# OK, ready to build the FME
/home/fmeuser/rebuild-fme.sh

Startup script, cron, and Apache

• The fme-tomcat4 script uses /home/fmeuser/tomcat4.conf to start the FME on boot

cp /home/fmeuser/fmesrc/fme-tomcat4 /etc/init.d
chkconfig --add fme-tomcat4
chkconfig fme-tomcat4 on

cat >> /etc/cron.d/fme-rebuild <<EOF
MAILTO=admin@sig.biostr.washington.edu
# rebuild the FME
00 00 * * Sun   fmeuser /home/fmeuser/rebuild-fme.sh
EOF

I also added this to /etc/httpd/conf.d/sig-local.conf so apache will redirect requests:

RedirectMatch ^/(FME/?)?(.*)$ http://fme.biostr.washington.edu:8089/FME/$2